crossing96/oncoscreening huggingface dataset:
The prediction of cancer-specific mortality in T1 non-muscle-invasive bladder cancer: comparison of logistic regression and artificial neural network: a SEER population-based study.	PURPOSE: To identify the risk factors for 5-year cancer-specific (CSS) and overall survival (OS) and to compare the accuracy of logistic regression (LR) and artificial neural network (ANN) in the prediction of survival outcomes in T1 non-muscle-invasive bladder cancer. METHODS: This is a population-based analysis using the Surveillance, Epidemiology, and End Results database. Patients with T1 bladder cancer (BC) who underwent transurethral resection of the tumour (TURBT) between 2004 and 2015 were included in the analysis. The predictive abilities of LR and ANN were compared. RESULTS: Overall 32,060 patients with T1 BC were randomly assigned to training and validation cohorts in the proportion of 70:30. There were 5691 (17.75%) cancer-specific deaths and 18,485 (57.7%) all-cause deaths within a median of 116 months of follow-up (IQR 80-153). Multivariable analysis with LR revealed that age, race, tumour grade, histology variant, the primary character, location and size of the tumour, marital status, and annual income constitute independent risk factors for CSS. In the validation cohort, LR and ANN yielded 79.5% and 79.4% accuracy in 5-year CSS prediction respectively. The area under the ROC curve for CSS predictions reached 73.4% and 72.5% for LR and ANN respectively. CONCLUSIONS: Available risk factors might be useful to estimate the risk of CSS and OS and thus facilitate optimal treatment choice. The accuracy of survival prediction is still moderate. T1 BC with adverse features requires more aggressive treatment after initial TURBT.	bladder
Clinical value of anoikis-related genes and molecular subtypes identification in bladder urothelial carcinoma and in vitro validation.	BACKGROUND: Anoikis is a programmed cell death process that was proven to be associated with cancer. Uroepithelial carcinoma of the bladder (BLCA) is a malignant disease of the urinary tract and has a strong metastatic potential. To determine whether anoikis-associated genes can predict the prognosis of BLCA accurately, we evaluated the prognostic value of anoikis-associated genes in BLCA and constructed the best model to predict prognosis. METHOD: The BLCA transcriptome data were downloaded from TCGA and GEO databases, and genes with differential expression were selected and then clustered using non-negative matrix factorization (NMF). The genes with the most correlation with anoikis were screened and identified using univariate Cox regression, lasso regression, and multivariate Cox regression. The GEO dataset was used for external validation. Nomograms were created based on risk characteristics in combination with clinical variants and the performance of the model was validated with receiver operating characteristic (ROC) curves. The immunotherapeutic significance of this risk score was assessed using the immune phenomenon score (IPS). IC50 values of predictive chemotherapeutic agents were calculated. Finally, we used RT-qPCR to determine the mRNA expression of four genes, CALR, FASN, CASP6, and RAD9A. RESULT: We screened 406 tumor samples and 19 normal tissue samples from the TCGA database. Based on anoikis-associated genes, we classified patients into two subtypes (C1 and C2) using NMF method. Subsequently, nine core genes were screened by multiple methods after analysis, which were used to construct risk profiles. The design of nomograms based on risk profiles and clinical variables, ROC, and calibration curves confirmed that the model could well have the ability to predict the survival of BLCA patients at 1, 3, and 5 years. By predicting the IC50 values of chemotherapeutic drugs, it was learned that the high-risk group (HRG) was more susceptible to paclitaxel, gemcitabine, and cisplatin, and the low-risk group (LRG) was more susceptible to veriparib and afatinib. CONCLUSION: In summary, the risk score of anoikis-associated genes can be applied as a predictor to predict the prognosis of BLCA in clinical practice.	bladder
A Restaging Transurethral Resection of Bladder Tumor Is Always Necessary For High-grade T1 Non-muscle-invasive Bladder Cancer.	Patients with high-grade T1 non-muscle-invasive bladder cancer (NMIBC) have a high risk of recurrence and upstaging. Restaging transurethral resection of bladder tumor allows better staging so that patients can proceed to the appropriate treatment in a timely manner. This should be done in all patients with high-grade T1 NMIBC.	bladder
Identification of necroptosis-related long non-coding RNAs prognostic signature and the crucial lncRNA in bladder cancer.	BACKGROUND: Research on the relationships between long non-coding RNAs (lncRNAs) and cancer is attractive and has progressed very rapidly. Necroptosis-related biomarkers can potentially be used for predicting the prognosis of cancer patients. This study aimed to establish a necroptosis-related lncRNA (NPlncRNA) signature to predict the prognosis of patients with bladder cancer (BCa). METHODS: First, NPlncRNAs were identified using Pearson correlation analysis and machine learning algorithms, including SVM-RFE, least absolute shrinkage and selection operator (LASSO) regression, and random forest. The prognostic NPlncRNA signature was constructed using univariate and multivariate Cox regression analyses and the diagnostic efficacy and clinically predictive efficiency were evaluated and validated. The biological functions of the signature were analysed using gene set enrichment analysis (GSEA) and functional enrichment analysis. We further integrated the RNA-seq dataset (GSE133624) with our outcomes to reveal the crucial NPlncRNA that was functionally verified by assessing cell viability, proliferation, and apoptosis in BCa cells. RESULTS: The prognostic NPlncRNAs signature was composed of PTOV1-AS2, AC083862.2, MAFG-DT, AC074117.1, AL049840.3, and AC078778.1, and a risk score based on this signature was proven to be an independent prognostic factor for the BCa patients, indicated by poor overall survival (OS) of patients in the high-risk group. Additionally, the NPlncRNAs signature had a higher diagnostic validity than that of other clinicopathological variables, with a greater area under the receptor operating characteristic and concordance index curves. A nomogram established by integrating clinical variables and risk score confirmed that the signature can accurately predict the OS of patients and has high clinical practicability. Functional enrichment analysis and GSEA revealed that some cancer-related and necroptosis-related pathways were enriched in high-risk groups. The crucial NPlncRNA MAFG-DT was associated with poor prognosis and was highly expressed in BCa cells. MAFG-DT silencing notably inhibited proliferation and enhanced apoptosis of BCa cells. CONCLUSIONS: A novel prognostic NPlncRNAs signature was identified in BCa in this study, which provides potential therapeutic targets among which MAFG-DT plays critical roles in the tumorigenesis of BCa.	bladder
Clinical Outcomes of Pelvic Lymph Node Dissection Before Versus After Robot-Assisted Laparoscopic Radical Cystectomy.	Objective: The purpose of this study was to compare the clinical outcomes of bladder cancer patients treated with extended pelvic lymph node dissection (ePLND) before or after cystectomy under robotic-assisted radical cystectomy (RARC). Methods: A retrospective study to identify 348 patients with bladder cancer who underwent RARC was performed. Of the patients, 152 (42.8%) underwent ePLND before radical cystectomy (RC) (group A) and 196 (56.3%) underwent ePLND after RC (group B). The clinical, pathological, and overall survival were compared. Results: The total and RC operation time in Group A (total: 130.68 ± 29.25 minutes, RC: 59.45 ± 28.63 minutes) were both shorter than Group B (total: 154.17 ± 38.18 minutes, RC: 94.81 ± 41.21 minutes) (P < .05). However, no significant difference in time of ePLND. The estimate blood loss (EBL) of RC part and total operation (RC+ePLND) in group A was less than group B (both P < .05), while the ePLND part did not show significance. The result of vascular and nerve injury and surgical drain withdrawal time were similar in two groups. The total number of lymph nodes in group A was fewer than group B (16 versus 26; P < .05). Moreover, the number of bilateral internal iliac and presacral lymph nodes of group A was fewer than group B significantly, whereas the number of bilateral external iliac, common iliac, and obturator lymph nodes was similar in two groups. The lymph node density of group A was significantly lower than group B. The median follow-up of all patients was 33.0 months. Importantly, the survival of group B was better than group A (hazard ratio: 1.412; 95% confidence interval: 1.004-1.987; P = .048). Conclusions: Performing ePLND before RC reveals better result on operation time and EBL, while, when ePLND after RC, the total number of lymph nodes dissected is more and the survival is better. It recommended ePLND be performed before RC, and it is necessary to recheck the internal iliac and presacral area after cystectomy.	bladder
A randomized controlled trial investigating rectus sheath catheters following radical cystectomy.	OBJECTIVE: To evaluate whether rectus sheath catheter (RSC) insertion may be an alternative to thoracic epidural (TE). PATIENTS AND METHODS: In a non-blinded, single-centre, non-inferiority study, patients undergoing open radical cystectomy were randomized 1:1 to receive either a TE or surgically placed RSC. The primary endpoint was cumulative opiate use (median oral morphine equivalent [OME]) in the first 72 h postoperatively. Secondary outcomes included visual analogue scale pain scores, measures of postoperative recovery including mobility and time to regular diet, and complications. RESULTS: Ninety-seven patients were randomized (51 TE, 46 RSC). The median OME was 103 (77.5-132.5) mg in the TE arm and 161.75 (117.5-187.5) mg in the RSC arm. A Mann-Whitney U-test confirmed non-inferiority of RSC to TE at a threshold of 15 mg OME (P = 0.002). When comparing pain scores for the first three postoperative days, an early difference was observed that favoured the TE group during post-anaesthesia care unit stay, which was lost after postoperative day 1. Patient satisfaction with analgesia on the third postoperative day was similar in the two arms (P = 0.47). There were no statistically significant differences between arms with respect to the other secondary outcomes. CONCLUSIONS: The outcomes from this prospective randomized trial demonstrated non-inferiority of RSC insertion compared to TE with respect to 72-h opiate use. Patient satisfaction with pain control on postoperative day 3 was the same for each group.	bladder
Checkpoint Inhibitors in Urothelial Carcinoma-Future Directions and Biomarker Selection.	CONTEXT: Several recent phase 2 and 3 trials have evaluated the efficacy and toxicity of checkpoint inhibitor (CPI) therapy for urothelial carcinoma (UC) in the metastatic, localized muscle-invasive UC (MIUC), upper tract UC, and non-muscle-invasive bladder cancer (NMIBC) disease state. OBJECTIVE: To assess the outcomes and toxicity of CPIs across the treatment landscape of UC and contextualize their application to current real-world treatment. EVIDENCE ACQUISITION: We queried PubMed, Web of Science, and EMBASE databases and conference abstracts to identify prospective trials examining CPIs in UC. The primary endpoints included overall survival, recurrence-free survival, and toxicity (when available). A secondary analysis included biomarker evaluation of response. EVIDENCE SYNTHESIS: We identified 21 trials, 12 phase 2 and nine phase 3 trials, in which a CPI was used for metastatic UC (seven), MIUC (nine), and NMIBC (five). For first-line (1L) metastatic UC, concurrent chemotherapy with CPIs failed to show superiority. Improved overall and progression-free survival for switch maintenance avelumab (after achieving stable disease or response with induction systemic chemotherapy) has established the current standard of care for 1L metastatic UC. A single-agent CPI is a consideration for patients unable to tolerate chemotherapy. CPIs in the perioperative setting are limited to only the adjuvant treatment with nivolumab after radical surgery for MIUC in patients at a higher risk of recurrence based on pathologic stage. Only pembrolizumab is approved by the Food and Drug Administration for carcinoma in situ unresponsive to bacillus Calmette-Guérin (BCG) in patients who are not fit for or who refuse radical cystectomy. Trials investigating CPIs in combination with multiple immune regulators, antibody drug conjugates, targeted therapies, antiangiogenic agents, chemotherapy, and radiotherapy are enrolling patients and may shape the future treatment of patients with UC. CONCLUSIONS: CPIs have an established role across multiple states of UC, with broadened applications likely to occur in the future. Several combinations are being evaluated, while the development of predictive biomarkers and their validation may help identify patients who are most likely to respond. PATIENT SUMMARY: Our findings highlight the broad activity of checkpoint inhibitors in urothelial carcinoma, noting the need for further investigation for the best application of combinations and patient selection to patient care.	bladder
Antibody-Drug Conjugates in the Treatment of Urothelial Cancer.	Antibody-drug conjugates (ADCs) have transformed the treatment landscape in oncology and become an essential therapeutic modality. In urothelial carcinoma (UC), the two ADCs that have been especially successful in clinical practice are enfortumab vedotin and sacituzumab govitecan. These drugs are currently approved as monotherapy for later lines of treatment in locally advanced or metastatic UC and have had a significant impact for patients with limited treatment options. Combinational trials, as well as additional ADCs, are currently being investigated in the treatment of UC for subsequent lines of therapy as overall survival rates remain dismal.	bladder
CD24 targeting with NK-CAR immunotherapy in testis, prostate, renal and (luminal-type) bladder cancer and identification of direct CD24 interaction partners.	Alternative therapeutic options targeting urologic malignancies, such as germ cell tumours, as well as urothelial, renal and prostate carcinomas, are still urgently needed. The membrane protein CD24 represents a promising immunotherapeutical approach. The present study aimed to decipher the molecular function of CD24 in vitro and evaluate the cytotoxic capacity of a third-generation natural killer (NK) cell chimeric antigen receptor (CAR) against CD24 in urologic tumour cell lines. Up to 20 urologic tumour cell lines and several non-malignant control cells were included. XTT viability assays and annexin V/propidium iodide flow cytometry analyses were performed to measure cell viability and apoptosis rates, respectively. Co-immunoprecipitation followed by mass spectrometry analyses identified direct interaction partners of CD24. Luciferase reporter assays were used to functionally validate transactivation of CD24 expression by SOX2. N- and O-glycosylation of CD24 were evaluated by enzymatic digestion and mass spectrometry. The study demonstrates that SOX2 transactivates CD24 expression in embryonal carcinoma cells. In cells of different urological origins, CD24 interacted with proteins involved in cell adhesion, ATP binding, phosphoprotein binding and post-translational modifications, such as histone acetylation and ubiquitination. Treatment of urological tumour cells with NK-CD24-CAR cells resulted in a decreased cell viability and apoptosis induction specifically in CD24(+) tumour cells. Limitations of the study include the in vitro setting, which still has to be confirmed in vivo. In conclusion, we show that CD24 is a promising novel target for immune therapeutic approaches targeting urologic malignancies.	bladder
Surveillance of prognostic risk factors in patients with SCCB using artificial intelligence: a retrospective study.	Small cell carcinoma of the bladder (SCCB) is a rare urological tumor. The prognosis of SCCB is abysmal. Therefore, this study aimed to construct nomograms that predict overall survival (OS) and cancer-specific survival (CSS) in SCCB patients. Information on patients diagnosed with SCCB during 2004-2018 was obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate Cox regression models analyzed Independent risk factors affecting patients' OS and CSS. Nomograms predicting the OS and CSS were constructed based on the multivariate Cox regression model results. The calibration curve verified the accuracy and reliability of the nomograms, the concordance index (C-index), and the area under the curve (AUC). Decision curve analysis (DCA) assessed the potential clinical value. 975 patients were included in the training set (N = 687) and the validation set (N = 288). Multivariate COX regression models showed that age, marital status, AJCC stage, T stage, M stage, surgical approach, chemotherapy, tumor size, and lung metastasis were independent risk factors affecting the patients' OS. However, distant lymph node metastasis instead AJCC stage is the independent risk factor affecting the CSS in the patients. We successfully constructed nomograms that predict the OS and CSS for SCCB patients. The C index of the training set and the validation set of the OS were 0.747 (95% CI 0.725-0.769) and 0.765 (95% CI 0.736-0.794), respectively. The C index of the CSS were 0.749 (95% CI 0.710-0.773) and 0.786 (95% CI 0.755-0.817), respectively, indicating that the predictive models of the nomograms have excellent discriminative power. The calibration curve and the AUC also show good accuracy and discrimination of the nomograms. To sum up, We established nomograms to predict the OS and CSS of SCCB patients. The nomograms have undergone internal cross-validation and show good accuracy and reliability. The DCA shows that the nomograms have an excellent clinical value that can help doctors make clinical-assisted decision-making.	bladder
Health outcomes and budget impact projection of anti-PD-(L)1s in cancer care in Portugal.	INTRODUCTION: PD-[L]1 inhibitors revolutionized cancer treatment but challenge the affordability of health systems. This policy-focused model aimed to estimate the health and budget impact of anti-PD-(L)1s in Portugal and inform current discussions. MATERIALS AND METHODS: The Health Impact Projection (HIP) model estimates clinical (life years, progression-free survival [PFS] years, and quality-adjusted life years [QALY] gained and adverse events [AEs] incurred) and economic (direct and indirect costs) outcomes in a world where cancer patients are initiating treatment with standard-of-care (SOC) versus SOC plus anti-PD-(L)1s over a 3-year time horizon. Indications included adjuvant and metastatic melanoma, non-small cell lung cancer (first and second line), metastatic triple-negative breast cancer, head and neck cancer, urothelial carcinoma, and renal cell carcinoma. Model inputs were based on publicly available literature data and expert opinion. RESULTS: The model estimated that, over 3 years, 7,773 patients would be treated with anti-PD-(L)1s, realizing a gain of 4,787 life years, 6,901 PFS years, and 4,214 QALYs and avoiding 399 AEs. The introduction of anti-PD-(L)1s had a projected average annual impact of ≈ €108 million and a share of 20% of total cancer medicines expenditure and 0.6% of total healthcare expenditure in 2021. Although higher disease management costs are expected for patients living longer with anti-PD-(L)1s and drug acquisition costs are considerable, that is partially offset by a reduction in end-of-life costs (€611,092/year) and costs associated with patient productivity lost to cancer (€9,128,142/year). DISCUSSION: This model highlights the significant survival and QoL benefit of anti-PD-(L)1s for cancer patients in Portugal, with a relatively low increased cost in total healthcare expenditure.	bladder
The Role of Fascin-1 in Human Urologic Cancers: A Promising Biomarker or Therapeutic Target?	Human cancer statistics show that an increased incidence of urologic cancers such as bladder cancer, prostate cancer, and renal cell carcinoma. Due to the lack of early markers and effective therapeutic targets, their prognosis is poor. Fascin-1 is an actin-binding protein, which functions in the formation of cell protrusions by cross-linking with actin filaments. Studies have found that fascin-1 expression is elevated in most human cancers and is related to outcomes such as neoplasm metastasis, reduced survival, and increased aggressiveness. Fascin-1 has been considered as a potential therapeutic target for urologic cancers, but there is no comprehensive review to evaluate these studies. This review aimed to provide an enhanced literature review, outline, and summarize the mechanism of fascin-1 in urologic cancers and discuss the therapeutic potential of fascin-1 and the possibility of its use as a potential marker. We also focused on the correlation between the overexpression of fascin-1 and clinicopathological parameters. Mechanistically, fascin-1 is regulated by several regulators and signaling pathways (such as long noncoding RNA, microRNA, c-Jun N-terminal kinase, and extracellular regulated protein kinases). The overexpression of fascin-1 is related to clinicopathologic parameters such as pathological stage, bone or lymph node metastasis, and reduced disease-free survival. Several fascin-1 inhibitors (G2, NP-G2-044) have been evaluated in vitro and in preclinical models. The study proved the promising potential of fascin-1 as a newly developing biomarker and a potential therapeutic target that needs further investigation. The data also highlight the inadequacy of fascin-1 to serve as a novel biomarker for prostate cancer.	bladder
The ablative effect of mitomycin reverse thermal gel: Expanding the role for nephron preservation therapy in low grade upper tract urothelial carcinoma.	PURPOSE: Assess the real-world ablative effect of mitomycin reverse thermal gel for low-grade upper tract urothelial carcinoma (UTUC) in patients who undergo biopsy only or partial ablation and evaluate utility of complete ablation prior to UGN-101. MATERIAL AND METHODS: We retrospectively reviewed low-grade UTUC patients treated with UGN-101 from 15 high-volume centers. Patients were categorized based on initial endoscopic ablation (biopsy only, partial ablation, or complete ablation) and by size of remaining tumor (complete ablation, <1cm, 1-3cm, or >3cm) prior to UGN-101. The primary outcome was rendered disease free (RDF) rate at first post-UGN-101 ureteroscopy (URS), defined as complete response or partial response with minimal mechanical ablation to endoscopically clear the upper tract of visible disease. RESULTS: One hundred and sixteen patients were included for analysis after excluding those with high-grade disease. At first post-UGN-101 URS, there were no differences in RDF rates between those who at initial URS (pre-UGN-101) had complete ablation (RDF 77.0%), partial ablation (RDF 55.9%) or biopsy only (RDF 66.7%) (P = 0.14). Similarly, a complimentary analysis focusing on tumor size (completely ablated, <1cm, 1-3cm or >3cm) prior to UGN-101 induction did not demonstrate significant differences in RDF rates (P = 0.17). CONCLUSION: The results of the early real-world experience suggest that UGN-101 may play a role in initial chemo-ablative cytoreduction of larger volume low-grade tumors that may not initially appear to be amenable to renal preservation. Further studies will help to better quantify the chemo-ablative effect and to identify clinical factors for patient selection.	bladder